Reactome is a free online database of biological pathways.[1][2][3] It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format.
Reactome is maintained by an international multidisciplinary team from OICR, OHSU, EMBL-EBI and NYULMC, with expertise in pathway curation and annotation, software development, and training and outreach, dedicated to providing the research community with openly accessible biological pathway knowledge. The Reactome project is led by Lincoln Stein (OICR). Peter D'Eustachio (NYULMC), Henning Hermjakob (EMBL-EBI), Guanming Wu (OHSU). The Reactome helpdesk can be reached via email.
Reactome: a database of reactions, pathways and biological processes.
Content
Description
Reactome: a database of reactions, pathways and biological processes.
Contact
Primary citation
PMID 37941124
Access
Data format
BioPAX SBML
Website
https://reactome.org
Download URL
https://reactome.org/download-data
Web service URL
https://reactome.org/ContentService/
Miscellaneous
License
https://reactome.org/license
Data release frequency
https://reactome.org/about/release-calendar
The website can be used to browse pathways and submit data to a suite of data analysis tools. The underlying data is fully downloadable in a number of standard formats including PDF, SBML, Neo4j GraphDB, MySQL, PSI-MITAB, and BioPAX. Pathway diagrams use a Process Description (PD) Systems Biology Graphical Notation (SBGN)-based style.
The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include signal transduction, innate and acquired immune function, transcriptional regulation, programmed cell death and classical intermediary metabolism.
The pathways represented in Reactome are species-specific, with each pathway step supported by literature citations that contain an experimental verification of the process represented. If no experimental verification using human reagents exists, pathways may contain steps manually inferred from non-human experimental details, but only if an expert biologist, named as Author of the pathway, and a second biologist, names as Reviewer, agree that this is a valid inference to make. The human pathways are used to computationally generate by an orthology-based process derived pathways in other organisms.
^Croft, D.; O'Kelly, G.; Wu, G.; Haw, R.; Gillespie, M.; Matthews, L.; Caudy, M.; Garapati, P.; Gopinath, G.; Jassal, B.; Jupe, S.; Kalatskaya, I.; Mahajan, S.; May, B.; Ndegwa, N.; Schmidt, E.; Shamovsky, V.; Yung, C.; Birney, E.; Hermjakob, H.; d'Eustachio, P.; Stein, L. (2010). "Reactome: A database of reactions, pathways and biological processes". Nucleic Acids Research. 39 (Database issue): D691–D697. doi:10.1093/nar/gkq1018. PMC 3013646. PMID 21067998.
^Joshi-Tope, G.; Gillespie, M.; Vastrik, I.; d'Eustachio, P.; Schmidt, E.; De Bono, B.; Jassal, B.; Gopinath, G.; Wu, G.; Matthews, L.; Lewis, S.; Birney, E.; Stein, L. (2004). "Reactome: A knowledgebase of biological pathways". Nucleic Acids Research. 33 (Database issue): D428–D432. doi:10.1093/nar/gki072. PMC 540026. PMID 15608231.
^Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P (2014). "The Reactome pathway knowledgebase". Nucleic Acids Res. 42 (Database issue): D472–7. doi:10.1093/nar/gkt1102. PMC 3965010. PMID 24243840.
Reactome is a free online database of biological pathways. It is manually curated and authored by PhD-level biologists, in collaboration with Reactome...
complete set of possible reactions constitutes its reactome. Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human...
vary between different database resources such as KEGG, WikiPathways, or Reactome. Also exist proprietary pathways collections used by e.g. Pathway Studio...
Database Netpath: curated resource of signal transduction pathways in humans Reactome: navigable map of human biological pathways, ranging from metabolic processes...
of IL-12 signaling can be found at the peer-reviewed pathway database Reactome: Interleukin-12 family IL-12 is linked with autoimmunity. Administration...
Research. "beta-ureidopropionate + H2O => beta-alanine + NH4+ + CO2". reactome. Archived from the original on 2013-10-23. Retrieved 2020-02-08. Cytosolic...
thousands of sequenced organisms KEGG: Kyoto Encyclopedia of Genes and Genomes Reactome, a database of reactions, pathways and biological processes MetaCyc: A...
McDowall/Interpro: Protein of the Month: Fibrinogen. Peter D'Eustachio/reactome: fibrinogen → fibrin monomer + 2 fibrinopeptide A + 2 fibrinopeptide B...
reconciles those resources: BiGG ChEBI enviPath HMDB GO KEGG LipidMaps MetaCyc Reactome Rhea SABIO-RK SwissLipids The SEED Ganter M, Bernard T, Moretti S, Stelling...
a database of biological pathways and interactions. Biological pathway Reactome Cerami, Ethan G; Gross Benjamin E; Demir Emek; Rodchenkov Igor; Babur Ozgün;...
"wiki" concept. All pathways have an open license and can be freely used. Reactome is a free and manually curated online database of biological pathways....
biological discovery. It is supported by a variety of online databases (e.g. Reactome) and tools. The latest released version is BioPAX Level 3. There is also...
1038/ncb2897. PMC 4354890. PMID 24366029. "Reactome | Activation of ATR in response to replication stress". www.reactome.org. Retrieved 2017-04-09. Allen C,...
Enrichment: Identify enriched biological themes, particularly GO terms, KEGG, Reactome, BioCarta, WikiPathways as well as other pathways and data sets collected...
is freely available for academic use under http://ConsensusPathDB.org. Reactome (metabolic and signaling pathways) KEGG (metabolic pathways only have been...
Gene Nomenclature Committee Mutant Mouse Resource and Research Centers Reactome - a curated knowledgebase of biological pathways Undiagnosed Diseases Program...
utilizing the gene regulation knowledge available from databases such as., Reactome and KEGG. High-throughput measurement technologies, such as microarray...
ATP-dependent RNA helicase activity Cellular Components nucleolus preribosomes Reactome Pathways major pathway of rRNA processing in the nucleolus and cytosol...
drug action pathways and 5) drug metabolism pathways. KEGG HMDB DrugBank Reactome MetaCyc List of biological databases Frolkis, A; Knox, C; Lim, E; Jewison...
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